Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

Ghebremedhin, Meron; Yesupriya, Shubha; Luka, Janos; Crane, Nicole J.

doi:10.1117/12.2076997

Cited by 4 publications

(2 citation statements)

References 35 publications

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“…Raman spectroscopy is a rapid and noninvasive vibrational spectroscopic technique that yields molecular fingerprint information from biological samples such as bacteria. Numerous studies have successfully identified bacteria at the strain level by using Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) spectral databases of the microorganisms ( 13 – 25 ). In our previous work ( 25 ), Raman spectra of 42 bacterial samples that encompassed a wide range of bacterial species (10 different genera) were analyzed.…”

Section: Introductionmentioning

confidence: 99%

“…Numerous studies have successfully identified bacteria at the strain level by using Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) spectral databases of the microorganisms ( 13 – 25 ). In our previous work ( 25 ), Raman spectra of 42 bacterial samples that encompassed a wide range of bacterial species (10 different genera) were analyzed. Models were developed and successfully validated using a test set at the Gram and genus taxonomic levels.…”

Section: Introductionmentioning

confidence: 99%

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Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study

et al. 2017

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In recent years, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has become the standard for routine bacterial species identification due to its rapidity and low costs for consumables compared to those of traditional DNA-based methods. However, it has been observed that strains of some bacterial species, such as Acinetobacter baumannii strains, cannot be reliably identified using mass spectrometry (MS). Raman spectroscopy is a rapid technique, as fast as MALDI-TOF, and has been shown to accurately identify bacterial strains and species. In this study, we compared hierarchical clustering results for MS, genomic, and antimicrobial susceptibility test data to hierarchical clustering results from Raman spectroscopic data for 31 A. baumannii clinical isolates labeled according to their pulsed-field gel electrophoresis data for strain differentiation. In addition to performing hierarchical cluster analysis (HCA), multiple chemometric methods of analysis, including principal-component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), were performed on the MS and Raman spectral data, along with a variety of spectral preprocessing techniques for best discriminative results. Finally, simple HCA algorithms were performed on all of the data sets to explore the relationships between, and natural groupings of, the strains and to compare results for the four data sets. To obtain numerical comparison values of the clustering results, the external cluster evaluation criteria of the Rand index of the HCA dendrograms were calculated. With a Rand index value of 0.88, Raman spectroscopy outperformed the other techniques, including MS (with a Rand index value of 0.58).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study

et al. 2017

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Diagnostic Bacteriology: Raman Spectroscopy

Pavlicek¹,

Crane

Ghebremedhin

et al. 2017

Methods in Molecular Biology

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Current clinical methodology for identification of bacterial infections relies predominantly on culturing microbes from patient material and performing biochemical tests. This can often be an inefficient and lengthy process, which has a significant detrimental effect upon patient care. Techniques used in other aspects of molecular research have the potential to revolutionize the way in which diagnostic tests are used and delivered in the clinical setting. The need for rapid, accurate, and cost-effective molecular techniques in the diagnostic laboratory is imperative to improving patient care, preventing the spread of drug resistance and decreasing the overall burden associated with nosocomial infections. Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) are powerful vibrational spectroscopy techniques that are being developed for highly sensitive pathogen identification in complex clinical samples. Raman spectroscopy is a molecular technique that is capable of probing samples noninvasively and nondestructively. It has been used with high specificity to assess tissue and bacterial samples at the molecular level with diverse clinical and diagnostic applications. SERS has recently developed out of the advances in the Raman spectroscopy arena. This technique is designed to amplify Raman scattering and allows for better differentiation of bacterial isolates. Although the current parameters for the use of SERS require a pure culture and are relatively monoparametric, current breakthroughs and testing are pushing the technology to new levels and thus changing the face of modern bacterial diagnostics.

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Surface enhanced Raman spectroscopy as a point-of-care diagnostic for infection in wound effluent

Ghebremedhin¹,

Yesupriya²,

Crane³

2016

SPIE Proceedings

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Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

Cited by 4 publications

References 35 publications

Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study

Accurate and Rapid Differentiation of Acinetobacter baumannii Strains by Raman Spectroscopy: a Comparative Study

Diagnostic Bacteriology: Raman Spectroscopy

Surface enhanced Raman spectroscopy as a point-of-care diagnostic for infection in wound effluent

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